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Host reaction of tomato varieties and applicability of Sm-linked DNA markers to Stemphylium lycopersici

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Abstract

Gray leaf spot (GLS) disease, caused by the Stemphylium (Sm) fungus, affects a wide range of horticultural crops including tomato. In this study, the South Korean Sm isolate (PNU-SM01) was identified, and the applicability of Sm-resistance gene (Sm)-linked DNA markers in marker-assisted selection was validated. ITS/gpd sequencing and morphological observation identified the isolate as S. lycopersici. A GLS disease assay was conducted on 80 tomato varieties, including commercial F1 hybrids and elite inbred lines. The reference line ‘Motelle’ was highly resistant (R, DSI = 4.0), whereas the ‘Moneymaker’ line was susceptible (S) and showed severe disease symptoms (DSI = 79.3). Among 30 commercial F1 hybrids, five were scored as S by DSI; whereas the rest, including all 17 hybrids claimed as Sm-resistant by the supplier, were R or moderately resistant (MR). Among 48 inbred lines, four were scored as S and 44, including five Lycopersicon accessions reported as R, were R or MR. Three known Sm-linked DNA markers (CT55, D5, and Sm-InDel) were genotyped in all 80 cultivars; the highest match (92.5%) to the GLS disease assay was observed for Sm-InDel. We converted the recessive marker CT55 into a codominant marker (CT55-Co) and developed dCAPS (Sm-SNP) and KASP (Sm-KASP) markers from a previously identified Sm-linked SNP. Sm-SNP and Sm-KASP showed a similar level of phenotype to marker genotype association as Sm-InDel, whereas CT55-Co displayed a high level of mismatch. To screen for the source of Sm resistance, 138 tomato accessions were genotyped with Sm-InDel and Sm-SNP: 15 were homozygous for the resistance allele of both markers. In this study, resistance to the Korean isolate of S. lycopersici in commercial F1 hybrids and breeding sources was characterized to reveal which DNA markers can be effectively applied for marker-assisted selection of Sm-resistance.

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Abbreviations

CAPS:

Cleaved amplified polymorphic sequence

dCAPS:

derived CAPS

DSI:

Disease severity index

GLS:

Gray leaf spot

ITS:

Internal transcribed spacer

KASP:

Kompetitive allele-specific PCR

MAS:

Marker-assisted selection

NCBI:

National Center for Biotechnology Information

PGBRC:

Plant Genetics and Breeding Research Center

RFLP:

Restriction fragment length polymorphism

SCAR:

Sequence characterized amplified region

SGN:

Sol Genomics Network

Sm:

Stemphylium

Sm :

Sm-resistance gene

SNP:

Single nucleotide polymorphism

LA:

Lycopersicon accession

TGRC:

Tomato Germplasm Research Center

VIGS:

Virus-induced gene silencing

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Funding

This research was supported by the Golden Seed Project (Center for Horticultural Seed Development, No. 2013007-05-1-SBF10), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA), and Korea Forest Service (KFS).

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Author notes

  1. Jiyeon Park and Seungahn Kwon contributed equally to this work.

Authors and Affiliations

  1. Department of Horticultural Bioscience, Pusan National University, Miryang, 50463, South Korea

    Jiyeon Park, Seungahn Kwon, Girim Park, Siyoung Lee, Byoung Il Je & Younghoon Park

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  1. Jiyeon Park
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  2. Seungahn Kwon
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  3. Girim Park
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  4. Siyoung Lee
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Correspondence to Younghoon Park.

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Supplementary Information

Table S1

Genotyping results of 138 tomato accessions using Sm-InDel and Sm-SNP. (XLSX 20 kb)

Fig. S1

Prediction of potential genes in the 80,294 bp genomic DNA of Solanum lycopersicum harboring the ORF9 sequence. (PDF 289 kb)

Fig. S2

Sequence alignment of ORF9 cloned from ‘Motelle’ and ‘Moneymaker’. (PDF 421 kb)

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Park, J., Kwon, S., Park, G. et al. Host reaction of tomato varieties and applicability of Sm-linked DNA markers to Stemphylium lycopersici. Mol Breeding 40, 106 (2020). https://doi.org/10.1007/s11032-020-01188-8

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